-
- if (hscroll.isVisible())
- {
- height += hscroll.getPreferredSize().height;
- }
- if (height > alignFrame.getHeight() / 2)
- {
- height = alignFrame.getHeight() / 2;
+
+ int theight = av.getCharHeight() * (av.getAlignment().getHeight() + (!av.hasHiddenRows() ? 0 : av.getAlignment().getHiddenSequences().getSize()));
+ float sscaling = (float) (theight/(1.0*theight+height));
+ float ascaling=(float)(height*1.0/alignFrame.getHeight());
+ int rheight = alignFrame.getHeight() - height - av.getCharHeight();
+ if (adjustPanelHeight)
+ {
+ // NOTE: this logic is different in the applet. Need a better algorithm to define behaviour
+ // try and set height according to alignment
+ if (ascaling>0 && sscaling < 0.5)
+ {
+ // if the alignment is too big then
+ // default is 0.5 split
+ height = alignFrame.getHeight() / 2;
+ }
+ else
+ {
+ // if space for more than one sequence row left when annotation is fully displayed then set height to annotation height
+ // otherwise, leave at least two lines of sequence shown.
+ height = (rheight>av.getCharHeight()) ? height : (-av.getCharHeight() * 3
+ + (int) (alignFrame.getHeight() * (1 - sscaling)));
+ }